The ultimate solution to your problem would be for mastodon to support true e2e encrypted DMs. That way it doesn’t put the mastodon operator in the position of being able to read, store, and possibly hand over DMs to law enforcement.
We made quite a few design decisions with Librem Social that differ from other Mastodon servers (how we handle timelines for instance) but we did them all for a reason and publicized and explained our reasoning. This is one of the big benefits of using a decentralized, federated service–a user isn’t locked in to us, they are free to choose whichever Mastodon server has the features, moderation, and other policies they prefer. We aren’t removing choice, instead we are adding an additional choice to the fediverse on top of all of the existing ones, for people who agree with our approach.
We didn’t want Librem Social users to have a false sense of privacy, we didn’t want to be put in the position of storing private-but-not-really messages, we offer an alternative for messaging that is secure with Matrix, and users who rely on unencrypted DMs can choose to set up a mastodon account on a different service that allows it.
Your point about possibly setting up an auto-respond so people know that DMs are disabled on our platform is a valid one, and it’s a shame that Mastodon doesn’t already have something like that in place.